Strain identifier

BacDive ID: 4341

Type strain: Yes

Species: Citrobacter youngae

Strain Designation: 460-61

Strain history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 460-61

NCBI tax ID(s): 133448 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7065

BacDive-ID: 4341

DSM-Number: 17578

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Citrobacter youngae 460-61 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from meat scraps.

NCBI tax id

  • NCBI tax id: 133448
  • Matching level: species

strain history

@refhistory
7065<- CIP <- P. A. D. Grimont, Institut Pasteur, Paris <- CDC
124017CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 460-61

doi: 10.13145/bacdive4341.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Citrobacter
  • species: Citrobacter youngae
  • full scientific name: Citrobacter youngae Brenner et al. 1993

@ref: 7065

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter youngae

full scientific name: Citrobacter youngae Brenner et al. 1993

strain designation: 460-61

type strain: yes

Morphology

cell morphology

  • @ref: 124017
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7065TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
36441MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
124017CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
124017CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7065positivegrowth30mesophilic
36441positivegrowth30mesophilic
50271positivegrowth37mesophilic
124017positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 124017
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12401729864mannitol+fermentation
12401716947citrate+carbon source
12401717716lactose-fermentation
12401717632nitrate+reduction
12401716301nitrite+reduction
12401715792malonate-assimilation
124017132112sodium thiosulfate+builds gas from
12401717234glucose+degradation

antibiotic resistance

  • @ref: 124017
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 124017
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12401715688acetoin-
12401717234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
124017oxidase-
124017beta-galactosidase+3.2.1.23
124017alcohol dehydrogenase-1.1.1.1
124017gelatinase-
124017catalase+1.11.1.6
124017lysine decarboxylase-4.1.1.18
124017ornithine decarboxylase-4.1.1.17
124017phenylalanine ammonia-lyase-4.3.1.24
124017tryptophan deaminase-
124017urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124017-+++-++-+-++-+-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124017++++++---++--+--++-+++-++----+-+-+--+--+---++--++++--+++++-++-------++---+-+---++-++--+-+++++++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7065meat scrapsSouth CarolinaUSAUSANorth America
50271Meat scrapsSouth CarolinaUSAUSANorth America
124017Food, Meat scrapsSouth CarolinaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Meat

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70652Risk group (German classification)
1240171Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter freundii 16S ribosomal RNAM592911490ena546
7065Citrobacter youngae partial 16S rRNA gene, strain CECT 5335AJ564736948ena133448

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter youngae CCUG 30791GCA_003818115contigncbi133448
66792Citrobacter youngae strain CCUG 30791133448.7wgspatric133448
66792Citrobacter youngae CCUG 307912903312461draftimg133448

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.672no
gram-positiveno98.438no
anaerobicno94.569no
halophileno91.789no
spore-formingno94.311no
glucose-utilyes94.58no
flagellatedyes54.735no
thermophileno99.256no
aerobicyes77.986no
glucose-fermentyes94.43no

External links

@ref: 7065

culture collection no.: CCUG 30791, DSM 17578, ATCC 29935, CDC 460-61, CECT 5335, CIP 105016

straininfo link

  • @ref: 73833
  • straininfo: 1753

literature

  • topic: Phylogeny
  • Pubmed-ID: 25687346
  • title: Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.
  • authors: Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000122
  • year: 2015
  • mesh: Bacterial Typing Techniques, Citrobacter/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7065Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17578
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36441Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16988
50271Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30791)https://www.ccug.se/strain?id=30791
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
73833Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1753.1StrainInfo: A central database for resolving microbial strain identifiers
124017Curators of the CIPCollection of Institut Pasteur (CIP 105016)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105016